Contacts of the strand formed by residues 57 - 65 (chain P) in PDB entry 1KD1
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 THR 57 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26P TRP* 6.2 0.4 - - + -
55P ASP 4.0 1.9 + - - -
56P GLU* 1.3 70.9 - - - +
58P VAL* 1.3 71.9 + - - +
59P VAL* 4.4 6.5 - - + -
75P THR* 3.4 35.2 - - + +
77P ALA* 4.2 14.4 - - + -
101P ALA* 5.6 4.7 - - + -
105P ASN* 5.5 4.9 + - - -
109P SER 5.5 1.6 + - - -
110P HIS 3.1 13.3 + - - -
111P VAL* 3.2 8.9 - - - +
112P ARG 2.8 25.2 + - - -
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Residues in contact with VAL 58 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48P ILE* 4.2 15.0 - - + -
52P ALA* 3.4 33.4 - - + -
56P GLU 4.2 6.7 - - - +
57P THR* 1.3 70.3 - - - +
59P VAL* 1.3 59.6 + - - +
60P VAL* 4.3 12.3 - - + -
74P VAL* 4.5 4.5 - - + -
75P THR 2.9 15.7 + - - +
76P VAL* 4.0 14.1 - - + +
77P ALA* 2.7 34.1 + - - +
112P ARG* 3.4 8.1 - - + +
114P ILE* 3.6 31.4 - - + -
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Residues in contact with VAL 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P VAL* 5.9 0.4 - - + -
26P TRP* 4.1 21.1 - - + -
29P VAL* 3.9 27.6 - - + -
57P THR* 4.1 9.4 - - + +
58P VAL* 1.3 77.9 - - - +
60P VAL* 1.3 66.3 + - - +
61P PRO* 3.3 6.4 - - + +
77P ALA* 3.5 10.1 - - + +
98P LEU* 4.2 10.8 - - + -
111P VAL* 3.1 32.5 - - + -
112P ARG 2.7 12.1 + - - +
113P VAL* 3.6 9.4 - - + +
114P ILE 3.2 20.1 + - - -
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Residues in contact with VAL 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P ALA* 4.0 4.0 - - + -
43P VAL* 3.8 26.7 - - + -
48P ILE* 4.6 5.2 - - + -
58P VAL* 4.3 9.6 - - + -
59P VAL* 1.3 76.2 - - - +
61P PRO* 1.3 54.1 - - - +
62P GLY 2.4 45.1 + - - +
63P LYS 3.9 7.6 - - - +
64P VAL* 3.7 19.1 - - + -
76P VAL* 4.3 12.8 - - + -
77P ALA 2.8 9.9 + - - -
78P ALA* 3.6 20.3 - - + -
79P VAL* 3.8 3.1 + - - +
98P LEU* 4.5 2.1 - - - +
114P ILE* 3.6 11.9 - - + +
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Residues in contact with PRO 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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721A A 6.0 0.4 - - + -
29P VAL* 4.1 32.5 - - + -
32P ARG* 4.0 26.2 - - + +
33P LEU* 3.7 16.1 - - + +
40P HIS* 4.1 4.5 - - - -
41P ALA* 3.3 25.0 + - + -
59P VAL* 3.3 12.9 - - + +
60P VAL* 1.3 78.6 - - + +
62P GLY* 1.3 55.8 + - - +
79P VAL* 4.8 0.9 - - + -
113P VAL* 4.2 14.6 - - + -
114P ILE 3.4 13.0 - - - +
115P ARG* 4.5 9.4 - - + +
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Residues in contact with GLY 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P LEU* 4.8 0.7 - - - -
40P HIS* 4.6 6.7 - - - -
41P ALA 3.3 13.9 - - - -
60P VAL* 2.4 26.8 + - - +
61P PRO 1.3 70.3 - - - -
63P LYS* 1.3 61.3 + - - -
78P ALA* 3.7 0.7 - - - +
79P VAL* 2.9 42.0 + - - +
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Residues in contact with LYS 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658A C 4.1 16.9 + - - +
659A A 2.8 73.9 + - - +
41P ALA 2.8 11.1 + - - +
42P GLU* 3.3 4.9 - - - -
43P VAL* 2.9 25.3 + - - -
60P VAL* 3.9 2.7 - - - +
62P GLY* 1.3 75.9 - - - +
64P VAL* 1.3 68.8 + - - +
65P LEU* 4.0 8.0 - - + +
79P VAL* 5.6 0.2 - - + -
80P ASP* 3.1 39.8 + - + +
82P SER 3.9 12.8 - - - +
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Residues in contact with VAL 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43P VAL* 3.1 9.9 - - + +
45P LEU* 3.8 26.7 - - + -
48P ILE* 3.9 11.7 - - + -
60P VAL* 3.7 21.8 - - + -
63P LYS* 1.3 77.9 - - - +
65P LEU* 1.3 66.9 + - - +
76P VAL* 4.2 5.2 - - + -
78P ALA* 3.6 24.0 - - + -
80P ASP 2.9 5.7 + - - -
81P PHE* 3.4 17.9 - - + -
82P SER 3.0 26.5 + - - -
85P ALA* 3.5 4.9 - - + +
89P ILE* 4.0 10.1 - - + -
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Residues in contact with LEU 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659A A 3.7 48.0 - - + +
660A A 3.5 7.0 - - - +
746A A 3.2 44.9 - - + +
42P GLU* 4.4 11.2 - - + -
43P VAL 2.5 12.9 + - - +
44P ASN* 2.9 36.3 - - - +
45P LEU* 3.3 9.7 + - - +
63P LYS* 4.0 16.4 - - + +
64P VAL* 1.3 82.0 - - - +
66P GLY* 1.3 59.8 + - - +
67P SER 3.3 1.0 + - - -
82P SER* 3.9 2.0 - - - -
85P ALA* 3.7 3.8 - - - -
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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
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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