Contacts of the strand formed by residues 47 - 56 (chain B) in PDB entry 6DVD
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 PRO 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B SER 4.4 2.5 - - - +
46B ILE* 1.3 89.7 - - + +
48B GLY* 1.3 57.4 + - - +
142B ARG* 3.8 30.2 + - + +
143B GLY 3.5 9.6 - - - +
144B ARG* 3.7 20.8 - - + +
170B PRO* 4.0 8.6 - - - +
210B SER* 5.0 4.3 - - - +
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Residues in contact with GLY 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE 3.3 2.4 + - - -
47B PRO* 1.3 74.1 - - - +
49B ALA* 1.3 59.8 + - - -
141B GLU 4.0 0.2 - - - +
142B ARG* 3.4 11.8 - - - +
143B GLY 2.8 33.4 + - - +
168B TYR* 3.2 21.1 + - - -
170B PRO* 4.4 7.2 - - - -
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLY* 1.3 74.3 - - - +
50B ALA* 1.3 65.7 + - - +
83B LEU 5.3 0.5 - - - +
85B VAL* 3.1 34.0 + - + +
86B SER* 4.2 1.4 - - - +
87B SER* 3.9 34.1 - - - +
140B VAL* 4.0 6.7 - - + -
141B GLU 3.4 14.4 - - - +
142B ARG* 4.7 3.8 - - + +
167B ILE 4.4 3.4 - - - +
168B TYR* 3.8 1.7 + - - -
199B LYS* 4.4 8.1 + - - -
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ALA* 1.3 77.9 - - - +
51B VAL* 1.3 69.3 + - - +
52B THR* 3.4 2.6 + - - -
81B LYS 5.3 5.2 - - - +
83B LEU 5.1 7.0 - - - +
85B VAL* 3.9 8.0 - - - +
140B VAL* 3.6 5.9 - - - -
141B GLU 3.4 25.9 + - - +
167B ILE* 3.3 39.0 - - + +
168B TYR* 4.0 9.2 - - + -
199B LYS* 5.3 0.9 - - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA* 1.3 74.6 - - - +
52B THR* 1.3 60.3 + - - +
53B SER 3.8 7.4 - - - +
54B ILE* 3.7 31.4 - - + -
80B LEU* 4.0 23.8 - - + +
81B LYS* 5.6 4.6 + - - +
83B LEU* 4.2 23.0 + - + +
138B LEU* 4.4 15.7 - - + -
139B VAL 3.2 15.9 - - - +
140B VAL* 4.5 9.9 - - + +
164B VAL* 3.3 19.9 - - + +
165B ASP 3.9 4.7 - - - +
166B SER* 3.4 11.3 + - - -
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Residues in contact with THR 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA 3.4 1.6 + - - -
51B VAL* 1.3 74.0 - - - +
53B SER* 1.3 58.6 + - - +
139B VAL* 2.6 16.7 + - - -
141B GLU* 3.1 51.5 + - - +
152B ASN* 3.5 30.8 + - + +
155B SER* 3.9 13.7 - - - +
163B PRO* 4.0 0.9 - - - +
164B VAL* 3.2 27.9 + - - +
166B SER* 3.6 4.6 + - - -
168B TYR* 3.4 8.7 + - - +
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 3.7 1.3 - - - +
52B THR* 1.3 82.9 - - - +
54B ILE* 1.3 68.2 + - - +
139B VAL* 2.9 47.0 + - - +
155B SER* 3.9 18.1 + - - -
156B GLY* 4.9 9.9 - - - -
161B ARG* 5.7 1.9 - - - +
162B ILE 3.3 16.8 - - - -
163B PRO* 3.9 9.2 - - - -
164B VAL* 4.3 2.7 - - - -
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Residues in contact with ILE 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 3.7 15.3 - - + -
53B SER* 1.3 79.5 - - - +
55B ARG* 1.3 64.1 + - - +
56B ILE* 4.1 21.3 - - + -
76B ILE* 4.8 0.9 - - + -
77B ILE* 4.1 16.8 - - + -
80B LEU* 3.8 26.0 - - + -
136B VAL* 4.2 1.6 - - + -
137B GLU 3.1 9.9 - - - +
138B LEU* 3.6 20.9 - - + -
139B VAL* 5.7 0.2 - - - -
161B ARG* 3.8 2.6 - - - +
162B ILE* 3.0 59.6 + - + +
164B VAL* 4.4 11.0 - - + -
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Residues in contact with ARG 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 1.3 76.6 - - - +
56B ILE* 1.3 65.9 + - - +
57B ASP 3.9 0.5 + - - -
96B TYR* 4.8 5.1 + - - -
136B VAL* 3.2 3.3 - - - -
137B GLU* 2.4 71.8 + - + +
157B ALA* 4.8 6.3 - - - +
159B ILE* 3.2 46.5 - - - +
160B GLY* 3.4 18.4 - - - +
161B ARG* 4.2 11.7 - - + -
162B ILE* 5.1 0.7 - - - -
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 4.1 20.9 - - + -
55B ARG* 1.3 80.2 - - - +
57B ASP* 1.3 74.4 + - - +
58B GLY 3.4 0.2 + - - -
59B VAL* 3.2 43.2 + - + +
66B VAL* 4.3 27.1 - - + -
73B VAL* 4.6 16.4 - - + -
76B ILE* 4.3 20.0 - - + -
134B LEU* 5.3 9.4 - - + -
135B GLU 3.6 8.5 - - - +
136B VAL* 3.8 16.4 - - + -
160B GLY 4.3 3.0 + - - -
162B ILE* 4.9 5.3 - - + +
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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