Contacts of the helix formed by residues 15 - 33 (chain K) in PDB entry 4XLN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 15 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1216J SER* 3.3 8.6 - - - +
1217J ILE* 2.8 40.0 + - - -
1481J VAL* 4.0 16.8 - - - -
13K VAL* 3.5 8.0 - - - +
14K ASP* 1.3 86.7 - - - +
16K LYS* 1.3 62.6 + - - +
17K TYR* 3.2 21.5 + - - +
18K ARG* 3.1 19.2 + - - +
19K LEU 3.5 3.3 + - - -
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Residues in contact with LYS 16 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043I TYR 4.7 3.2 + - - -
710J ARG* 4.4 11.9 - - - +
761J ILE* 5.0 0.8 - - + +
762J GLN* 4.3 17.5 + - + +
1208J ASP* 3.7 4.1 + - - -
1211J MET* 3.3 44.3 - - + +
1216J SER* 3.3 22.2 + - - +
1219J GLU* 3.3 19.3 + - - -
10K PHE* 3.8 27.8 - - + +
13K VAL* 5.1 1.3 - - - -
14K ASP 3.9 1.6 + - - -
15K SER* 1.3 71.0 + - - +
17K TYR* 1.3 91.2 + - + +
19K LEU* 3.1 12.8 + - - +
20K THR* 2.9 30.0 + - - +
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Residues in contact with TYR 17 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1043I TYR 3.1 14.7 + - - -
1044I GLY* 3.2 21.1 - - - -
762J GLN* 3.1 24.7 - - - -
1216J SER* 3.9 3.1 - - - -
1217J ILE 3.6 8.1 - - - +
1218J GLY 4.3 0.4 - - - -
1219J GLU* 2.6 58.8 + - + -
1475J GLY* 3.3 20.9 - - - +
1476J THR* 3.4 6.6 - - + -
1481J VAL* 3.7 20.2 - - + -
15K SER* 3.1 21.7 - - - +
16K LYS* 1.3 95.2 - - + +
18K ARG* 1.3 58.4 + - - +
20K THR* 3.3 7.4 + - - -
21K VAL* 2.9 33.3 + - - +
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Residues in contact with ARG 18 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1480J PHE* 3.0 49.5 + - - -
1481J VAL* 3.6 19.7 - - + +
1484J THR* 3.1 37.7 + - + +
13K VAL* 3.9 19.5 - - + -
14K ASP* 3.6 26.4 + - - -
15K SER* 3.1 13.5 + - - +
17K TYR* 1.3 76.4 - - - +
19K LEU* 1.3 60.3 + - - +
21K VAL* 3.3 4.4 + - - +
22K VAL* 2.9 34.2 + - + +
75K PHE* 5.3 4.9 - - + -
76K GLY* 4.8 2.6 - - - -
77K GLU* 3.9 26.6 + - - +
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Residues in contact with LEU 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761J ILE* 4.2 12.6 - - + -
6K ILE* 4.4 3.4 - - + -
9K LEU* 3.7 37.9 - - + +
10K PHE* 3.5 35.0 - - + -
12K MET* 5.8 0.7 - - + -
13K VAL* 3.6 21.1 - - + +
15K SER 3.5 2.2 + - - -
16K LYS* 3.1 9.5 + - - +
18K ARG* 1.3 78.9 - - - +
20K THR* 1.3 58.0 + - - +
22K VAL* 3.1 7.6 + - - +
23K VAL* 2.9 49.6 + - + +
68K LEU* 3.9 21.8 - - + -
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Residues in contact with THR 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754J PHE* 4.7 2.2 - - + +
757J ALA* 4.0 5.4 - - + +
758J GLU* 3.6 32.8 - - + +
761J ILE* 3.7 22.5 - - - +
762J GLN* 3.2 35.6 + - - +
1476J THR* 3.7 7.9 - - + -
16K LYS 2.9 13.5 + - - -
17K TYR 3.5 7.9 - - - -
19K LEU* 1.3 76.7 - - - +
21K VAL* 1.3 58.1 + - - +
23K VAL* 3.5 1.7 + - - +
24K ALA* 2.9 28.4 + - - +
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Residues in contact with VAL 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754J PHE* 4.0 20.6 - - + -
1476J THR* 3.6 24.9 - - - +
1481J VAL* 3.3 29.4 - - + +
1482J ARG* 4.4 2.9 - - - -
1484J THR* 3.7 11.0 - - - +
17K TYR 2.9 19.5 + - - +
18K ARG 3.6 7.0 - - - +
20K THR* 1.3 74.9 - - - +
22K VAL* 1.3 62.7 + - - +
24K ALA* 3.3 1.0 + - - +
25K LYS* 2.9 52.4 + - + +
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Residues in contact with VAL 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484J THR* 3.6 22.9 - - + -
1486J VAL* 3.5 23.8 - - + +
13K VAL* 5.4 2.0 - - + -
18K ARG* 2.9 25.2 + - + +
19K LEU* 3.3 10.1 - - - +
21K VAL* 1.3 77.6 - - - +
23K VAL* 1.3 65.7 + - - +
25K LYS 3.3 0.2 + - - -
26K ARG* 2.9 25.8 + - + +
68K LEU* 3.6 33.2 - - + -
73K LEU* 5.8 2.0 - - + -
75K PHE* 4.2 21.1 - - + -
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Residues in contact with VAL 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757J ALA* 4.4 2.5 - - + -
761J ILE* 3.8 13.2 - - + -
9K LEU* 5.5 0.2 - - + -
19K LEU* 2.9 35.9 + - + +
20K THR 3.8 3.8 - - - +
22K VAL* 1.3 74.3 - - + +
24K ALA* 1.3 58.6 + - - +
26K ARG* 4.6 0.9 - - - -
27K ALA* 2.9 29.1 + - - +
61K VAL* 3.9 26.2 - - + +
64K ALA* 3.5 22.5 - - + +
65K MET* 3.6 35.4 - - + -
68K LEU* 5.0 3.8 - - + -
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Residues in contact with ALA 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753J SER* 4.3 7.1 - - - -
754J PHE* 3.5 47.1 - - + -
757J ALA* 4.0 9.8 - - + +
20K THR 2.9 18.6 + - - +
21K VAL 3.5 4.5 - - - +
23K VAL* 1.3 77.3 - - - +
25K LYS* 1.3 58.1 + - - +
27K ALA* 3.3 2.7 + - - +
28K GLN* 2.9 32.3 + - - +
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Residues in contact with LYS 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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754J PHE* 4.8 13.5 - - + -
1482J ARG 3.3 21.5 + - - -
1483J PHE* 4.0 2.4 + - - +
1484J THR 2.4 37.6 + - - +
1485J GLN* 4.7 8.5 - - - +
1486J VAL* 4.1 14.4 - - + +
21K VAL* 2.9 35.1 + - + +
22K VAL 3.9 2.0 - - - +
24K ALA* 1.3 76.6 - - - +
26K ARG* 1.3 58.3 + - - +
28K GLN* 3.2 10.2 - - - +
29K GLN* 2.9 34.8 + - + +
82K GLU* 5.9 0.6 + - - -
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Residues in contact with ARG 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486J VAL* 3.6 21.2 - - + +
1488J ASP* 3.3 32.5 + - - +
22K VAL* 2.9 20.0 + - + +
23K VAL* 4.0 3.1 - - - +
25K LYS* 1.3 73.5 - - - +
27K ALA* 1.3 60.9 + - - +
29K GLN* 2.8 34.0 + - - -
30K LEU* 2.9 35.1 + - - +
37K ASN* 3.1 35.4 + - - +
39K VAL* 3.5 4.0 - - - +
64K ALA* 4.1 11.4 - - + +
67K GLU* 2.8 41.8 + - - +
73K LEU* 3.4 23.5 - - + +
89K MET* 4.1 0.4 - - - +
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Residues in contact with ALA 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753J SER* 4.4 12.3 - - - +
23K VAL 2.9 20.1 + - - +
24K ALA* 3.6 4.0 - - - +
26K ARG* 1.3 72.3 - - - +
28K GLN* 1.3 60.5 + - - +
30K LEU* 3.1 6.6 + - - +
31K LEU* 2.9 33.6 + - - +
60K ALA* 3.7 31.2 - - + +
61K VAL* 3.9 11.4 - - + +
64K ALA* 3.7 6.4 - - + +
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Residues in contact with GLN 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1075I ASP* 2.9 46.1 + - - +
1076I VAL 5.5 1.6 + - - -
753J SER* 4.7 4.6 - - - -
754J PHE* 5.8 4.3 - - + +
24K ALA 2.9 17.6 + - - +
25K LYS* 3.2 13.5 - - - +
27K ALA* 1.3 75.8 - - - +
29K GLN* 1.3 57.1 + - + +
31K LEU* 3.1 11.5 + - - +
32K ARG* 2.9 43.2 + - - +
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Residues in contact with GLN 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486J VAL* 3.0 30.9 + - - +
1487J VAL* 4.8 0.6 - - - +
1488J ASP* 4.8 0.2 - - - +
25K LYS* 2.9 20.3 + - + +
26K ARG* 2.8 41.6 + - - +
28K GLN* 1.3 76.9 - - + +
30K LEU* 1.3 62.1 + - - +
32K ARG* 3.3 14.2 + - - +
33K HIS* 3.3 14.8 + - - +
37K ASN* 3.2 20.4 + - - +
85K LEU* 5.3 11.3 - - - +
89K MET* 3.6 25.7 - - + +
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Residues in contact with LEU 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K ARG* 2.9 43.2 + - - +
27K ALA* 3.1 9.6 + - - +
29K GLN* 1.3 76.7 - - - +
31K LEU* 1.3 57.7 + - - +
34K ARG* 3.1 6.8 + - - -
35K PHE* 2.9 47.7 + - + -
37K ASN* 3.4 22.4 - - - +
38K THR* 4.9 2.2 - - - -
60K ALA* 4.1 3.8 - - + +
63K TRP* 3.5 36.6 - - + -
64K ALA* 3.9 8.5 - - + +
67K GLU* 3.3 25.4 - - - +
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Residues in contact with LEU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1073I GLY 5.7 4.9 - - - +
1074I GLU* 5.3 4.9 - - - +
1075I ASP* 4.5 21.1 - - + +
753J SER* 3.3 26.2 - - - +
27K ALA 2.9 13.7 + - - +
28K GLN* 3.1 11.6 + - - +
30K LEU* 1.3 77.9 - - - +
32K ARG* 1.3 64.4 + - - +
34K ARG* 3.4 17.0 + - + +
35K PHE* 5.2 4.9 - - + -
58K PRO 5.0 7.4 - - - +
60K ALA* 3.6 21.3 - - + -
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Residues in contact with ARG 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K GLN* 2.9 27.7 + - - +
29K GLN* 3.3 13.4 + - - +
31K LEU* 1.3 79.3 - - - +
33K HIS* 1.3 68.7 + - + +
34K ARG* 3.7 2.8 + - - +
86K GLN* 4.2 15.2 - - - +
90K GLU* 3.3 44.7 + - + +
94K PRO 5.0 6.9 - - - +
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Residues in contact with HIS 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K GLN* 3.3 22.9 + - - -
32K ARG* 1.3 83.8 + - + +
34K ARG* 1.3 72.5 + - - +
35K PHE 3.6 0.2 - - - -
36K LYS* 3.7 14.0 + - - +
37K ASN* 3.5 34.3 - - + +
89K MET* 3.3 46.3 + - + +
90K GLU* 3.2 29.6 + - - +
93K TYR* 3.7 34.1 + + + +
94K PRO* 5.0 12.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il