Contacts of the strand formed by residues 117 - 126 (chain A) in PDB entry 4PHZ
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 ASP 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A TYR* 2.5 35.4 + - - +
67A VAL 3.0 6.1 - - - +
68A HIS* 2.9 39.2 - - - +
115A GLY 3.9 2.3 - - - +
116A LYS* 1.3 74.3 - - - +
118A TYR* 1.3 65.9 + - - +
270A PRO* 3.1 12.0 - - - +
271A ILE* 3.0 37.8 + - + +
276A THR* 4.8 5.3 + - + +
277A VAL* 4.2 23.0 + - - +
391A LEU* 4.9 0.9 - - - +
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Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LYS* 3.2 2.9 - - - +
67A VAL* 2.6 42.6 + - + +
69A VAL* 3.8 24.7 - - + -
101A ILE* 4.0 21.1 - - + -
102A GLY* 4.0 8.7 - - - +
111A SER 4.4 1.3 + - - -
112A LEU* 4.0 14.0 - - + -
113A GLU* 2.9 40.5 + - - +
116A LYS* 3.5 24.5 - - + +
117A ASP* 1.3 79.1 - - - +
119A ALA* 1.3 58.8 + - - +
268A LEU* 3.6 41.1 - - + -
269A THR 5.3 0.2 - - - -
270A PRO* 4.0 21.2 - - + +
271A ILE* 3.6 7.6 - - - +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLY 3.3 12.6 - - - +
66A LYS* 4.0 7.0 - - + +
100A PHE 4.6 0.2 - - - -
101A ILE* 3.3 2.8 - - - -
102A GLY* 3.2 24.5 + - - +
103A GLU* 4.4 3.0 + - + -
118A TYR* 1.3 73.4 - - - +
120A PHE* 1.3 60.3 + - - +
269A THR 5.8 0.2 + - - -
271A ILE* 3.7 20.8 - - + +
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 3.7 27.1 - + - -
48A VAL* 4.6 4.9 - - + -
63A LEU* 4.8 3.4 - - + -
64A SER* 3.5 9.5 - - - -
65A GLY* 2.8 66.3 + - - +
66A LYS* 3.6 11.9 - - - -
67A VAL* 4.3 4.5 - - + -
85A LEU* 4.0 20.6 - - + -
100A PHE* 3.0 15.3 - - - +
101A ILE* 3.8 22.9 - - + -
118A TYR 4.6 0.7 - - - -
119A ALA* 1.3 76.3 - - - +
121A SER* 1.3 70.4 + - - +
122A ILE* 4.6 6.7 - - + -
136A ALA* 3.8 30.3 - - + -
138A ILE* 5.2 0.4 - - + -
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Residues in contact with SER 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 5.2 7.2 - - - -
63A LEU 3.1 6.1 - - - -
64A SER* 3.4 20.6 - - - +
99A GLN* 3.1 4.0 - - - +
100A PHE* 2.8 48.9 + - - +
120A PHE* 1.3 79.7 - - - +
122A ILE* 1.3 65.1 + - - +
123A ASN* 5.4 3.4 + - - -
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A VAL* 3.3 3.6 - - - -
63A LEU* 2.6 55.6 + - + +
85A LEU* 3.8 26.2 - - + -
86A ASN 3.7 29.6 - - - +
87A ALA* 4.2 10.8 - - + +
96A ARG* 4.2 16.4 - - - -
98A ALA 3.6 9.6 - - - +
99A GLN* 4.0 2.9 - - + +
120A PHE* 4.6 6.1 - - + -
121A SER* 1.3 79.8 - - - +
123A ASN* 1.3 64.5 + - - +
124A LEU* 3.5 27.7 + - + +
136A ALA* 5.0 2.2 - - - -
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Residues in contact with ASN 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLU* 3.4 18.8 - - + +
61A MET 3.5 4.5 - - - +
62A VAL* 3.2 24.4 - - - +
96A ARG* 3.5 3.5 - - - -
97A THR* 2.7 37.2 + - + +
98A ALA* 2.8 37.7 + - - +
100A PHE* 3.9 15.0 - - - -
121A SER* 5.4 3.3 + - - -
122A ILE* 1.3 72.5 + - - +
124A LEU* 1.3 59.6 + - - +
179B HIS* 5.0 4.2 - - - -
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Residues in contact with LEU 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU 4.1 0.5 - - - +
60A GLU* 3.4 3.9 - - - +
61A MET* 2.7 54.8 + - + +
63A LEU* 4.6 17.0 - - + -
87A ALA* 4.2 16.6 - - + -
89A GLU* 4.7 1.1 - - - +
94A LEU* 3.8 31.5 - - + +
95A VAL 3.7 1.3 - - - -
96A ARG* 3.7 28.9 - - + +
122A ILE* 3.5 19.0 + - + +
123A ASN* 1.3 74.8 - - - +
125A ARG* 1.3 59.4 + - - +
134A VAL* 3.9 28.0 - - + -
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASN* 2.4 61.8 + - - +
59A GLU 3.7 3.8 - - - -
60A GLU* 3.8 22.7 + - - +
94A LEU* 3.1 5.1 - - - -
95A VAL* 2.7 48.0 + - + +
97A THR* 4.2 7.9 - - - +
124A LEU* 1.3 72.5 - - - +
126A GLY* 1.3 65.2 + - - +
162A PHE* 3.8 16.3 - - + -
163A THR* 3.2 21.5 + - - -
164A ASP* 2.9 31.2 + - - -
165A PRO* 5.1 1.6 - - - +
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Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A VAL* 4.3 2.2 - - - -
56A ASN 4.1 11.4 - - - -
57A VAL* 3.5 5.1 - - - -
58A ASN 2.9 23.6 + - - -
59A GLU 3.1 14.8 + - - -
94A LEU* 3.4 16.9 - - - +
125A ARG* 1.3 69.6 - - - +
127A ARG* 1.3 57.2 + - - -
155A ILE* 4.1 11.7 - - - -
162A PHE* 3.0 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
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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