Contacts of the strand formed by residues 61 - 71 (chain K) in PDB entry 3STJ
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 PHE 61 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31K VAL* 3.7 25.1 - - + -
32K GLU* 3.4 6.9 - - - +
33K GLY* 3.2 34.1 + - - +
34K THR 3.3 42.0 - - - -
59K GLN* 4.6 1.6 - - - +
60K PRO* 1.3 75.9 - - - +
62K GLU* 1.3 67.8 + - - +
63K GLY* 3.9 10.8 - - - -
83K VAL 5.7 0.7 - - - -
86K GLN* 3.7 47.6 - - + -
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Residues in contact with GLU 62 (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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30K ARG* 3.2 34.1 + - + +
31K VAL 3.3 3.4 - - - +
32K GLU* 3.2 36.1 - - + +
61K PHE* 1.3 77.2 - - - +
63K GLY* 1.3 60.1 + - - +
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Residues in contact with GLY 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K VAL 4.4 0.2 - - - -
30K ARG* 3.6 6.4 - - - +
31K VAL* 2.9 43.4 + - - +
61K PHE* 3.9 11.1 - - - -
62K GLU* 1.3 73.6 - - - +
64K LEU* 1.3 62.2 + - - +
65K GLY 4.4 0.2 - - - -
83K VAL* 5.6 3.8 - - - -
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Residues in contact with LEU 64 (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 SER* 3.7 17.5 - - - +
29K VAL 3.3 8.7 - - - +
30K ARG* 4.4 20.6 - - + +
63K GLY* 1.3 71.9 - - - +
65K GLY* 1.3 67.2 + - - +
83K VAL* 4.9 2.5 - - - -
146K ASN* 3.7 31.4 - - + +
149K GLY* 4.1 19.1 - - - +
185K GLY* 3.7 17.1 - - - -
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Residues in contact with GLY 65 (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 SER* 3.7 4.3 - - - -
29K VAL* 2.9 29.2 + - - +
64K LEU* 1.3 80.3 - - - +
66K SER* 1.3 66.0 + - - -
83K VAL* 3.9 19.1 - - - +
146K ASN* 4.0 0.9 - - - +
185K GLY* 3.6 11.4 - - - -
187K SER* 3.8 6.7 - - - -
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Residues in contact with SER 66 (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 VAL* 5.0 0.9 - - - -
27K VAL 3.3 12.6 - - - -
29K VAL* 3.6 8.5 - - - +
65K GLY* 1.3 75.0 + - - -
67K GLY* 1.3 56.9 + - - +
79K THR* 2.8 27.9 + - - -
144K VAL 4.8 0.2 - - - -
145K GLY* 3.2 9.3 - - - -
146K ASN* 2.8 31.5 + - - +
185K GLY 3.1 7.0 + - - -
186K ASN 4.0 0.8 + - - -
187K SER 2.7 13.4 + - - +
188K GLY 3.4 4.0 - - - -
189K GLY* 3.6 22.9 - - - -
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Residues in contact with GLY 67 (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 VAL* 3.4 11.0 - - - +
27K VAL* 2.8 44.6 + - - +
29K VAL* 3.8 3.3 - - - +
66K SER* 1.3 76.5 - - - +
68K VAL* 1.3 63.2 + - - -
77K VAL* 3.9 5.4 - - - -
78K LEU 3.2 13.0 - - - -
188K GLY 3.3 2.7 + - - -
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Residues in contact with VAL 68 (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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25K ALA 3.7 4.7 - - - +
26K VAL* 4.6 2.2 - - + +
67K GLY* 1.3 78.8 - - - +
69K ILE* 1.4 63.7 + - - +
70K ILE* 3.3 3.9 + - + +
77K VAL* 3.3 5.3 - - - +
78K LEU* 2.8 43.6 + - + +
127K ILE* 3.7 42.0 - - + -
188K GLY 3.8 8.5 - - - +
189K GLY 3.8 1.1 - - - -
190K ALA* 3.5 37.0 - - + +
198K LEU* 4.1 15.9 - - + -
201K ILE* 4.4 5.6 - - + -
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Residues in contact with ILE 69 (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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24K PRO 4.1 7.9 - - - +
25K ALA* 2.8 16.9 + - - +
27K VAL* 3.6 28.0 - - + -
68K VAL* 1.4 67.5 - - - +
70K ILE* 1.3 59.9 + - - +
71K ASN 3.8 6.3 - - - +
72K ALA* 3.8 27.8 - - - +
76K TYR 3.5 7.2 - - - +
77K VAL* 3.9 15.0 - - + -
94K LEU* 4.2 7.4 - - + -
118K ILE* 4.5 2.9 - - + -
124K LEU* 3.9 26.2 - - + -
125K THR 3.3 28.0 - - - +
126K GLN* 3.4 1.2 - - - -
127K ILE* 2.9 32.1 + - - +
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Residues in contact with ILE 70 (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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68K VAL* 3.3 7.1 + - + +
69K ILE* 1.3 74.3 - - - +
71K ASN* 1.4 62.0 + - + +
76K TYR* 2.8 31.0 + - + +
78K LEU* 3.6 33.2 - - + +
115K LEU* 4.4 10.5 - - + -
126K GLN* 3.9 16.6 - - - +
127K ILE* 4.4 11.9 - - + +
129K ILE* 3.7 33.5 - - + +
198K LEU* 5.2 2.2 - - + -
225K ARG* 4.8 7.0 - - + -
228K ALA* 4.2 14.1 - - + -
232K ILE* 5.3 5.2 - - + -
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Residues in contact with ASN 71 (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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69K ILE* 3.8 3.4 - - - +
70K ILE* 1.4 78.7 - - + +
72K ALA* 1.3 53.5 + - - +
73K SER* 3.1 14.8 + - - -
74K LYS* 3.0 40.0 + - - +
75K GLY* 2.8 31.4 + - - -
76K TYR* 3.0 36.0 + - + -
126K GLN* 3.4 7.9 + - - +
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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
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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