Contacts of the strand formed by residues 73 - 78 (chain D) in PDB entry 6DWM
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 VAL 73 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D PRO* 4.1 21.1 - - + -
41D PRO* 3.5 21.0 - - - +
70D TYR 4.0 6.2 - - - +
71D GLY 3.3 0.6 - - - -
72D ASP* 1.3 82.3 - - + +
74D LEU* 1.3 63.4 + - - +
84D VAL* 4.2 15.7 - - + -
85D VAL 3.9 2.2 - - - -
86D LEU* 4.3 4.9 - - + -
91D THR* 3.6 22.2 - - + -
396D LEU* 4.0 17.9 - - + +
397D LYS* 4.6 5.2 - - + -
399D PHE* 3.9 32.5 - - + -
401D ILE* 4.6 7.6 - - + -
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PRO* 4.0 4.7 - - - -
41D PRO 3.3 13.2 - - - +
42D GLY* 5.1 0.9 - - - -
43D PRO* 5.9 0.4 - - + -
63D LEU* 4.7 3.8 - - + +
66D MET* 4.1 18.2 - - + +
67D SER* 3.7 28.7 - - - +
70D TYR* 4.0 15.3 - - + -
71D GLY 3.7 17.9 - - - +
73D VAL* 1.3 74.8 - - - +
75D GLN* 1.3 63.0 + - - +
76D ILE* 4.0 18.2 - - + -
84D VAL* 3.4 8.7 - - - +
85D VAL* 2.9 59.9 + - + +
87D SER* 4.8 2.0 - - - +
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Residues in contact with GLN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASN* 4.5 6.8 - - - +
40D PRO* 3.4 40.9 - - + +
41D PRO 2.9 6.2 + - - +
42D GLY* 3.5 19.6 - - - -
43D PRO* 4.2 1.4 - - - +
51D HIS* 4.9 0.9 - - - -
74D LEU* 1.3 75.0 - - - +
76D ILE* 1.3 80.5 + - - +
77D ARG* 5.9 1.1 - - + +
82D PRO* 3.7 23.6 - - + +
83D VAL 3.4 12.1 - - - +
84D VAL* 4.7 4.5 - - + -
405D ARG* 4.1 15.1 - - - +
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Residues in contact with ILE 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PRO* 4.7 0.7 - - + -
51D HIS* 3.8 24.7 - - + +
55D LEU* 4.3 22.0 - - + -
63D LEU* 4.1 12.6 - - + -
66D MET* 3.7 31.0 - - + -
74D LEU* 4.0 7.2 - - + -
75D GLN* 1.3 82.8 - - - +
77D ARG* 1.3 72.7 + - - +
78D ILE* 4.6 8.7 - - + -
82D PRO* 3.4 2.4 - - - +
83D VAL* 2.8 48.8 + - + +
85D VAL* 4.0 19.1 - - + -
408D PHE* 5.2 2.2 - - + -
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Residues in contact with ARG 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLY* 3.3 24.2 + - - +
46D TRP 2.5 31.9 + - - -
47D PRO* 3.6 15.1 + - - +
50D GLY* 3.4 3.7 - - - -
51D HIS* 2.8 46.6 + - + +
75D GLN* 5.9 1.1 - - + +
76D ILE* 1.3 82.0 - - - +
78D ILE* 1.3 65.9 + - - +
79D GLY 3.0 28.7 + - - +
80D SER* 4.4 10.9 - - - +
81D THR 3.4 6.5 - - - +
82D PRO* 4.2 16.4 - - + -
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Residues in contact with ILE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D ILE 4.0 1.8 - - - -
51D HIS 5.8 0.2 - - - -
52D MET* 4.3 24.7 - - + +
55D LEU* 4.3 18.8 - - + -
76D ILE* 4.6 6.3 - - + -
77D ARG* 1.3 74.4 - - - +
79D GLY* 1.3 63.7 + - - +
80D SER 3.3 0.3 + - - -
81D THR* 3.0 19.5 + - - -
83D VAL* 4.2 9.9 - - + -
231D GLY* 4.2 12.8 - - - +
233D PRO* 4.9 6.1 - - + -
236D PHE* 3.2 65.9 - - + +
237D ILE* 5.4 0.2 - - + -
408D PHE* 4.2 22.0 - - + -
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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